Mercurial > repos > ebi-gxa > seurat_run_tsne
annotate seurat_macros.xml @ 1:13a27436f8ee draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author | ebi-gxa |
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date | Mon, 25 Nov 2019 06:11:40 -0500 |
parents | 3aea769deab1 |
children | fd0fc93b3c87 |
rev | line source |
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3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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1 <?xml version="1.0"?> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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2 <macros> |
1
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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3 <token name="@VERSION@">0.0.6</token> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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4 <token name="@SEURAT_VERSION@">3.1.1</token> |
0
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
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5 <xml name="requirements"> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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changeset
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6 <requirements> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
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8 </requirements> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
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9 </xml> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff
changeset
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10 <xml name="version"> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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11 <version_command><![CDATA[ |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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13 ]]></version_command> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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changeset
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14 </xml> |
3aea769deab1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
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15 |
1
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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16 <xml name="input_object_params"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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17 <conditional name="input" label="Input format"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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18 <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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diff
changeset
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20 <option value="loom">Loom</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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changeset
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21 <option value="anndata">AnnData</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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diff
changeset
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22 <option value="rds_sce">RDS with a Single Cell Experiment object</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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changeset
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23 </param> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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changeset
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24 <when value="anndata"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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25 <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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diff
changeset
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26 </when> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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diff
changeset
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27 <when value="loom"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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changeset
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28 <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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29 </when> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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diff
changeset
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30 <when value="rds_seurat"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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31 <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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32 </when> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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33 <when value="rds_sce"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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34 <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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35 </when> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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36 </conditional> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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37 </xml> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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38 |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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39 <token name="@INPUT_OBJECT@"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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40 #if $input.format == "anndata" |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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41 --input-object-file '$input.anndata_file' --input-format anndata |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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42 #else if $input.format == "loom" |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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43 --input-object-file '$input.loom_file' --input-format loom |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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44 #else if $input.format == "rds_seurat" |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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45 --input-object-file '$input.rds_seurat_file' --input-format seurat |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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46 #else if $input.format == "rds_sce" |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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47 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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48 #end if |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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49 </token> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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50 |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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51 <xml name="output_object_params"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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52 <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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53 <option value="rds_seurat" selected="true">RDS with a Seurat object</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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54 <option value="loom">Loom</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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55 <option value="rds_sce">RDS with a Single Cell Experiment object</option> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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56 </param> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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57 </xml> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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58 |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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59 <xml name="output_files"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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60 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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61 <filter>format == 'loom'</filter> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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62 </data> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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63 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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64 <filter>format == 'rds_seurat'</filter> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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65 </data> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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66 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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67 <filter>format == 'rds_sce'</filter> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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68 </data> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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69 </xml> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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70 |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
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71 <token name="@OUTPUT_OBJECT@"> |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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72 #if $format == "anndata" |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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73 --output-object-file '$anndata_file' --output-format anndata |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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74 #else if $format == "loom" |
13a27436f8ee
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents:
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75 --output-object-file seurat_obj.loom --output-format loom |
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76 #else if $format == "rds_seurat" |
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77 --output-object-file '$rds_seurat_file' --output-format seurat |
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78 #else if $format == "rds_sce" |
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79 --output-object-file '$rds_sce_file' --output-format singlecellexperiment |
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80 #end if |
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81 </token> |
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82 |
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83 <xml name="genes-use-input"> |
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84 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/> |
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85 </xml> |
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86 <xml name="dims-use-input"> |
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87 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/> |
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88 </xml> |
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89 |
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90 <token name="@SEURAT_INTRO@"><![CDATA[ |
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91 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. |
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92 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and |
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93 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse |
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94 types of single cell data. |
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95 ]]></token> |
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96 |
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97 <token name="@VERSION_HISTORY@"><![CDATA[ |
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98 **Version history** |
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99 |
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100 3.1.1_0.0.6+galaxy0: Moved to Seurat 3. |
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101 |
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102 Find clusters: removed dims-use, k-param, prune-snn. |
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103 |
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104 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at |
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105 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l). |
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106 |
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107 0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9. |
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108 ]]></token> |
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109 |
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110 |
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111 <xml name="citations"> |
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112 <citations> |
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113 <citation type="doi">10.1038/nbt.4096</citation> |
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114 <citation type="bibtex"> |
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115 @misc{r-seurat-scripts.git, |
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116 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team}, |
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117 year = {2018}, |
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118 title = {Seurat-scripts: command line interface for Seurat}, |
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119 publisher = {GitHub}, |
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120 journal = {GitHub repository}, |
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121 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, |
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122 } |
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123 </citation> |
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124 </citations> |
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125 </xml> |
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126 </macros> |